RosettaCommons
about inpainting details
Hi, developers
i am trying to play the inpainting method, i use the test case 2KL8.pdb，and i keep the contigs from A2-8 and to rebuild the left structure.
what i use the command:
!python inpaint.py --task hal --checkpoint v02
--pdb=./test/input/2KL8.pdb
--out=./test/output/inpaint_test2
--contigs A2-8 --len 100
--num_designs 1
--inf_method=multi_shot --n_iters 10 --recycle_str_mode both --clamp_1d 0.1 --dump_all
result: Generating design 0 (1 total)... mask_str (1=rebuild; 0=keep): 1111111111111111111111111111111111111111111100000001111111111111111111111111111111111111111111111111 mask_seq (1=rebuild; 0=keep): 1111111111111111111111111111111111111111111100000001111111111111111111111111111111111111111111111111 0 LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLEMDIRFRLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL 1 KLLLLLLLLKELLLKLLLKLLLKLLKKLKLLLLELLELLLKLLEEMDIRFRLLLLLLLELLLELLEELLELLLLLLKKLLLLLLLLLLLLLLLLLLLLLL 2 SLKLEESLLLLELLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLEMDIRFRLNLELLEELLELLLELLLLLLELLKLLLLLLLLLLLLLLLLLLLLLLLL 3 KLKLEELLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLEMDIRFRLLLELLEELLELLLELLLLLLELLLELLLLLLLLLLLLLLLLLLLLLLL 4 SLLLKLKLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLKLLLEMDIRFRLLLELLLELLELLLELLLLLLLLLLKLLLLLLLLLLLLLLLLLLLLLLL 5 KLKLPESLLLLLLLLLLLLLLLLLLLKLKLSLLLLKLLLELLLKEMDIRFRLSGELLEELLELLLELLELLLELLLLLLLLLLLLLLLLLLLLLLLLLLL 6 SLKLLELLLLLLLLLLLLLLLLLLLLGLKLSLLLLLKLLELLLEEMDIRFRLLLGLLLLLLELLLELLELLLELLLLLLLLLLLLLLLLLLLLLLLLLLL 7 SLKLLELLLLLELLLLLLLLLLLLLLGLKLSLLNLKKLLKLLLEEMDIRFRLLLGLNLELLELLLLLLLLLLELLLLLLLLLLLLLLLLLLLLLLLLLLL 8 SLKLLELSLLLELLLLLLLLLLLLLLLLKLSLLNLLELLELLLKEMDIRFRLLLGLNLELLELLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL 9 SLKLLELSLLLELLLLLLLLLLLLLLKLKLSLLLLLELLKLLLKEMDIRFRLLLGPLLELLELLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL Designed sequence (excluding receptor): SLKLLELSLLLELLLLLLLLLLLLLLKLKLSLLLLLELLKLLLKEMDIRFRLLLGPLLELLELLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL Saving outputs for /content/RFDesign/inpainting/test/output/inpaint_test2_0: pdb npz fas trb Finished design in 7.80 seconds. Max CUDA memory: 2.1457G
after 10 iters, the sequence seem abnormal, can you giving me some suggestions to make it better？
thanks, weikun
This output is expected. These inpainting checkpoints aren't good at building regions longer than ~20 residues.
If you, for instance, use --window A,2,8 (rebuild that region only), you'll get more sensible results.
If you want to scaffold a motif into a larger protein, you should use hallucination. We currently only use inpainting to diversify small regions of structure & sequence in a protein that has already been designed using other methods. We are currently training some networks that are better at longer-region inpainting; those will probably be released with the published version of the paper.
On Sat, Jan 15, 2022 at 8:20 PM guyu @.***> wrote:
Hi, developers
i am trying to play the inpainting method, i use the test case 2KL8.pdb，and i keep the contigs from A2-8 and to rebuild the left structure.
what i use the command:
!python inpaint.py --task hal --checkpoint v02 --pdb=./test/input/2KL8.pdb --out=./test/output/inpaint_test2 --contigs A2-8 --len 100 --num_designs 1 --inf_method=multi_shot --n_iters 10 --recycle_str_mode both --clamp_1d 0.1 --dump_all
result: Generating design 0 (1 total)... mask_str (1=rebuild; 0=keep):
1111111111111111111111111111111111111111111100000001111111111111111111111111111111111111111111111111 mask_seq (1=rebuild; 0=keep):
1111111111111111111111111111111111111111111100000001111111111111111111111111111111111111111111111111 0 LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLEMDIRFRLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL 1 KLLLLLLLLKELLLKLLLKLLLKLLKKLKLLLLELLELLLKLLEEMDIRFRLLLLLLLELLLELLEELLELLLLLLKKLLLLLLLLLLLLLLLLLLLLLL 2 SLKLEESLLLLELLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLEMDIRFRLNLELLEELLELLLELLLLLLELLKLLLLLLLLLLLLLLLLLLLLLLLL 3 KLKLEELLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLEMDIRFRLLLELLEELLELLLELLLLLLELLLELLLLLLLLLLLLLLLLLLLLLLL 4 SLLLKLKLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLKLLLEMDIRFRLLLELLLELLELLLELLLLLLLLLLKLLLLLLLLLLLLLLLLLLLLLLL 5 KLKLPESLLLLLLLLLLLLLLLLLLLKLKLSLLLLKLLLELLLKEMDIRFRLSGELLEELLELLLELLELLLELLLLLLLLLLLLLLLLLLLLLLLLLLL 6 SLKLLELLLLLLLLLLLLLLLLLLLLGLKLSLLLLLKLLELLLEEMDIRFRLLLGLLLLLLELLLELLELLLELLLLLLLLLLLLLLLLLLLLLLLLLLL 7 SLKLLELLLLLELLLLLLLLLLLLLLGLKLSLLNLKKLLKLLLEEMDIRFRLLLGLNLELLELLLLLLLLLLELLLLLLLLLLLLLLLLLLLLLLLLLLL 8 SLKLLELSLLLELLLLLLLLLLLLLLLLKLSLLNLLELLELLLKEMDIRFRLLLGLNLELLELLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL 9 SLKLLELSLLLELLLLLLLLLLLLLLKLKLSLLLLLELLKLLLKEMDIRFRLLLGPLLELLELLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL Designed sequence (excluding receptor):
SLKLLELSLLLELLLLLLLLLLLLLLKLKLSLLLLLELLKLLLKEMDIRFRLLLGPLLELLELLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL Saving outputs for /content/RFDesign/inpainting/test/output/inpaint_test2_0: pdb npz fas trb Finished design in 7.80 seconds. Max CUDA memory: 2.1457G
after 10 iters, the sequence seem abnormal, can you giving me some suggestions to make it better？
thanks, weikun
— Reply to this email directly, view it on GitHub https://github.com/RosettaCommons/RFDesign/issues/2, or unsubscribe https://github.com/notifications/unsubscribe-auth/AABCU53YWADGFBG6IUTD5ILUWJBPTANCNFSM5MBZWXIA . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.
You are receiving this because you are subscribed to this thread.Message ID: @.***>
